Job ID = 6458381 SRX = SRX507393 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:37:11 prefetch.2.10.7: 1) Downloading 'SRR1213180'... 2020-06-21T12:37:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:37:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:37:45 prefetch.2.10.7: 'SRR1213180' is valid 2020-06-21T12:37:45 prefetch.2.10.7: 1) 'SRR1213180' was downloaded successfully Read 4185532 spots for SRR1213180/SRR1213180.sra Written 4185532 spots for SRR1213180/SRR1213180.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:02 4185532 reads; of these: 4185532 (100.00%) were unpaired; of these: 290696 (6.95%) aligned 0 times 3040498 (72.64%) aligned exactly 1 time 854338 (20.41%) aligned >1 times 93.05% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 1233339 / 3894836 = 0.3167 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 21:40:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 21:40:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:31: 1000000 INFO @ Sun, 21 Jun 2020 21:40:37: 2000000 INFO @ Sun, 21 Jun 2020 21:40:41: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:40:41: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:40:41: #1 total tags in treatment: 2661497 INFO @ Sun, 21 Jun 2020 21:40:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:40:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:40:41: #1 tags after filtering in treatment: 2661142 INFO @ Sun, 21 Jun 2020 21:40:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:40:41: #1 finished! INFO @ Sun, 21 Jun 2020 21:40:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:40:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:40:41: #2 number of paired peaks: 1713 INFO @ Sun, 21 Jun 2020 21:40:41: start model_add_line... INFO @ Sun, 21 Jun 2020 21:40:41: start X-correlation... INFO @ Sun, 21 Jun 2020 21:40:42: end of X-cor INFO @ Sun, 21 Jun 2020 21:40:42: #2 finished! INFO @ Sun, 21 Jun 2020 21:40:42: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 21:40:42: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 21:40:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.05_model.r INFO @ Sun, 21 Jun 2020 21:40:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:40:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:40:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:40:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:40:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:40:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.05_summits.bed INFO @ Sun, 21 Jun 2020 21:40:51: Done! pass1 - making usageList (567 chroms): 2 millis pass2 - checking and writing primary data (5087 records, 4 fields): 20 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 21:40:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 21:40:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:01: 1000000 INFO @ Sun, 21 Jun 2020 21:41:07: 2000000 INFO @ Sun, 21 Jun 2020 21:41:11: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:41:11: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:41:11: #1 total tags in treatment: 2661497 INFO @ Sun, 21 Jun 2020 21:41:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:41:11: #1 tags after filtering in treatment: 2661142 INFO @ Sun, 21 Jun 2020 21:41:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:12: #2 number of paired peaks: 1713 INFO @ Sun, 21 Jun 2020 21:41:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:12: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 21:41:12: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 21:41:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.10_model.r INFO @ Sun, 21 Jun 2020 21:41:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.10_summits.bed INFO @ Sun, 21 Jun 2020 21:41:22: Done! pass1 - making usageList (456 chroms): 1 millis pass2 - checking and writing primary data (1177 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 21:41:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 21:41:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:31: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:41:37: 2000000 INFO @ Sun, 21 Jun 2020 21:41:41: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:41:41: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:41:41: #1 total tags in treatment: 2661497 INFO @ Sun, 21 Jun 2020 21:41:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:41:41: #1 tags after filtering in treatment: 2661142 INFO @ Sun, 21 Jun 2020 21:41:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:41: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:42: #2 number of paired peaks: 1713 INFO @ Sun, 21 Jun 2020 21:41:42: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:42: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:42: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:42: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:42: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 21:41:42: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 21:41:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.20_model.r INFO @ Sun, 21 Jun 2020 21:41:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:41:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507393/SRX507393.20_summits.bed INFO @ Sun, 21 Jun 2020 21:41:52: Done! pass1 - making usageList (185 chroms): 1 millis pass2 - checking and writing primary data (296 records, 4 fields): 9 millis CompletedMACS2peakCalling